NWB conversion tools

NWB Conversion Tools is a package for creating NWB files by converting and combining neural data in proprietary formats and adding essential metadata.

Under heavy construction. API is changing rapidly.

Features:

• Command line interface
• Python API
• Leverages SpikeExtractor to support conversion from a number or proprietary formats.

Installation

To install nwb-conversion-tools directly in an existing environment:

$ pip install nwb-conversion-tools

Alternatively, to clone the repository and set up a conda environment, do:

$ git clone https://github.com/catalystneuro/nwb-conversion-tools
$ cd nwb-conversion-tools
$ conda env create -f make_env.yml
$ conda activate nwb_conversion_env
$ pip install .

Dependencies

NWB Conversion Tools relies heavily on SpikeExtractors for electrophysiology and on ROIExtractors for optophysiology data.

You can use a graphical interface for your converter with NWB Web GUI.

Rebuilding on Read the Docs

As a maintainer, once the changes to the documentation are on the master branch, go to https://readthedocs.org/projects/nwb-conversion-tools/ and click "Build version". Check the console output and its log for any errors.

Catalogue

v0.9.3

Buzsáki Lab: buzsaki-lab-to-nwb

This project is an ongoing effort for the Ripple U19 conversion of extracellular electrophysiology data to NWB format, including final publishing of each dataset on DANDI. Currently spans 7 major publications and over 14 TB of data on the DANDI Archive. Most of the data consists of raw recordings, LFP, spike sorted units, and behavior with can consist of a mix of mental state tracking, position tracking through mazes, and trial stimulus events.

Shenoy Lab: shenoy-lab-to-nwb:

v0.9.2

Brody Lab: brody-lab-to-nwb

The Brody lab has a long history with extracellular electrophysiology experiements spanning multiple acquisition systems. This project served two purposes - to allow the conversion of older data from Neuralynx and SpikeGadgets to NWB, and also their newer, larger data using Neuropixels (SpikeGLX). These recordings, some of which exceeded more than 250 GB (several hours worth!), were paired with rich trials tables containing catagorical events and temporal stimuli.

v0.8.10

Feldman Lab: feldman-lab-to-nwb

The Feldman lab utilizes a Neuropixels (SpikeGLX) system along with multiple sophisticated behavior systems for manipulating whisker stimulation in mice. These give rise to very complex trials tables tracking multiple event times throughout the experiments, including multiple event trains within trials.

v0.8.1

Hussaini Lab: hussaini-lab-to-nwb

v0.7.2

Movson lab: movshon-lab-to-nwb

v0.7.0

Tank Lab: tank-lab-to-nwb

Neuropixel (SpikeGLX) recordings of subjects navigating a virtual reality! Behavior contains a huge variety of NWB data types including positional and view angle over time, collision detection, and more! Paired with a specific extension for parsing experiment metadata.

Groh lab: mease-lab-to-nwb

Utilizing the CED recording interface, this project paired ecephys channels with optogenetic stimulation via laser pulses, and mechnical pressure stimulation over time - all of which are channels of data extracted from the common .smrx files!

Giocomo lab: giocomo-lab-to-nwb

Other labs that use NWB standard

• Axel lab: axel-lab-to-nwb
• Brunton lab: brunton-lab-to-nwb
• Buffalo lab: buffalo-lab-data-to-nwb
• Jaeger lab: jaeger-lab-to-nwb
• Tolias lab: tolias-lab-to-nwb